Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains

The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.

Automated summary

The discovery of the ability of experimental dsRNA delivery to induce gene silencing has revolutionized genetics research. However, the efficacy of this RNA interference (RNAi) varies within the natural population of Caenorhabditis elegans, raising questions about the understanding of RNAi in the lab compared to its activity in nature. This study investigates why some wild strains of C. elegans do not mount a strong RNAi response to germline targets. The results demonstrate functional diversification in the small RNA pathways in C. elegans, suggesting that RNAi processes are rapidly evolving in nature.